Multiple sequence alignment - TraesCS1B01G032200

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Download Multiple Sequence Alignment: (Fasta) (Clustal)



BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1B01G032200 chr1B 100.000 7752 0 0 1 7752 15654288 15662039 0.000000e+00 14316.0
1 TraesCS1B01G032200 chr1B 97.965 1081 17 3 682 1761 16184501 16183425 0.000000e+00 1869.0
2 TraesCS1B01G032200 chr1B 96.542 1012 33 1 3074 4083 16182520 16181509 0.000000e+00 1674.0
3 TraesCS1B01G032200 chr1B 95.104 531 22 1 6537 7063 16180248 16179718 0.000000e+00 833.0
4 TraesCS1B01G032200 chr1B 99.351 308 2 0 6201 6508 16180551 16180244 6.790000e-155 558.0
5 TraesCS1B01G032200 chr1B 96.259 294 10 1 7273 7565 458136674 458136381 1.510000e-131 481.0
6 TraesCS1B01G032200 chr1B 95.238 294 13 1 7273 7565 37792820 37793113 1.520000e-126 464.0
7 TraesCS1B01G032200 chr1B 93.897 213 12 1 1 213 583165374 583165163 3.490000e-83 320.0
8 TraesCS1B01G032200 chr1B 94.805 154 7 1 7600 7752 16176588 16176435 1.010000e-58 239.0
9 TraesCS1B01G032200 chr1B 98.837 86 0 1 7054 7138 16179364 16179279 1.350000e-32 152.0
10 TraesCS1B01G032200 chr1B 100.000 80 0 0 3002 3081 16183439 16183360 1.740000e-31 148.0
11 TraesCS1B01G032200 chr1B 97.143 35 1 0 7566 7600 626303012 626302978 8.400000e-05 60.2
12 TraesCS1B01G032200 chr1B 97.143 35 0 1 7566 7600 142286515 142286548 3.020000e-04 58.4
13 TraesCS1B01G032200 chr2B 95.163 1199 54 2 1761 2959 55033010 55034204 0.000000e+00 1890.0
14 TraesCS1B01G032200 chr2B 93.118 1206 76 6 1753 2956 159097324 159096124 0.000000e+00 1760.0
15 TraesCS1B01G032200 chr2B 94.816 1061 50 4 1757 2815 246118350 246117293 0.000000e+00 1650.0
16 TraesCS1B01G032200 chr2B 96.259 294 10 1 7273 7565 17266954 17266661 1.510000e-131 481.0
17 TraesCS1B01G032200 chr2B 94.811 212 9 1 5 214 451904641 451904852 5.800000e-86 329.0
18 TraesCS1B01G032200 chr2B 97.436 39 1 0 7566 7604 17266619 17266581 5.020000e-07 67.6
19 TraesCS1B01G032200 chr2B 97.222 36 0 1 7566 7601 756192969 756192935 8.400000e-05 60.2
20 TraesCS1B01G032200 chr4B 93.884 1210 58 8 1756 2965 489980697 489981890 0.000000e+00 1810.0
21 TraesCS1B01G032200 chr4B 96.928 293 7 2 7273 7565 481627595 481627885 2.510000e-134 490.0
22 TraesCS1B01G032200 chr1A 92.988 1198 71 10 1761 2956 249431093 249429907 0.000000e+00 1735.0
23 TraesCS1B01G032200 chr1A 91.829 1126 83 4 4414 5539 12835770 12834654 0.000000e+00 1561.0
24 TraesCS1B01G032200 chr1A 82.971 1057 93 38 723 1726 12859093 12858071 0.000000e+00 874.0
25 TraesCS1B01G032200 chr1A 83.931 753 108 7 6075 6823 12818907 12818164 0.000000e+00 708.0
26 TraesCS1B01G032200 chr1A 84.821 672 62 13 3303 3967 12856868 12856230 2.360000e-179 640.0
27 TraesCS1B01G032200 chr1A 85.111 497 58 9 213 696 12859642 12859149 1.940000e-135 494.0
28 TraesCS1B01G032200 chr1A 83.940 467 60 8 3953 4419 12856213 12855762 4.300000e-117 433.0
29 TraesCS1B01G032200 chr1A 93.056 216 13 2 1 214 59591858 59591643 1.620000e-81 315.0
30 TraesCS1B01G032200 chr1A 79.765 425 72 13 4207 4627 12772137 12771723 5.880000e-76 296.0
31 TraesCS1B01G032200 chr1A 89.062 64 7 0 6014 6077 12818993 12818930 6.450000e-11 80.5
32 TraesCS1B01G032200 chr6B 95.177 1099 48 4 1757 2854 710067215 710068309 0.000000e+00 1731.0
33 TraesCS1B01G032200 chr6B 95.205 292 13 1 7273 7563 40574640 40574931 1.970000e-125 460.0
34 TraesCS1B01G032200 chr6B 97.222 36 1 0 7566 7601 52975286 52975251 2.340000e-05 62.1
35 TraesCS1B01G032200 chrUn 97.082 994 26 2 1761 2754 38952738 38951748 0.000000e+00 1672.0
36 TraesCS1B01G032200 chr3B 97.989 945 19 0 1761 2705 586749037 586748093 0.000000e+00 1640.0
37 TraesCS1B01G032200 chr3B 93.607 219 12 2 1 218 223525483 223525700 7.500000e-85 326.0
38 TraesCS1B01G032200 chr3B 97.059 34 0 1 7566 7599 715507336 715507304 1.000000e-03 56.5
39 TraesCS1B01G032200 chr5D 94.177 1082 51 8 1763 2839 296995341 296994267 0.000000e+00 1639.0
40 TraesCS1B01G032200 chr5D 94.884 215 10 1 1 214 393815238 393815024 1.250000e-87 335.0
41 TraesCS1B01G032200 chr5D 94.884 215 10 1 1 214 393849564 393849350 1.250000e-87 335.0
42 TraesCS1B01G032200 chr7D 95.238 294 13 1 7273 7565 634239635 634239342 1.520000e-126 464.0
43 TraesCS1B01G032200 chr7D 75.490 714 145 16 5307 6011 18588748 18589440 9.700000e-84 322.0
44 TraesCS1B01G032200 chr7D 82.065 184 26 6 5307 5488 18631106 18631284 4.850000e-32 150.0
45 TraesCS1B01G032200 chr7D 97.297 37 1 0 752 788 18609970 18610006 6.490000e-06 63.9
46 TraesCS1B01G032200 chr5B 95.238 294 13 1 7273 7565 399219491 399219784 1.520000e-126 464.0
47 TraesCS1B01G032200 chr5B 95.238 294 13 1 7273 7565 595290070 595289777 1.520000e-126 464.0
48 TraesCS1B01G032200 chr5B 92.308 221 12 3 1 216 102595857 102595637 7.550000e-80 309.0
49 TraesCS1B01G032200 chr5B 97.059 34 0 1 7566 7599 91185167 91185199 1.000000e-03 56.5
50 TraesCS1B01G032200 chr7B 94.898 294 14 1 7273 7565 146255707 146256000 7.090000e-125 459.0
51 TraesCS1B01G032200 chr4A 75.456 713 147 18 5307 6011 714192931 714192239 9.700000e-84 322.0
52 TraesCS1B01G032200 chr4A 93.488 215 12 2 1 213 513330482 513330268 1.260000e-82 318.0
53 TraesCS1B01G032200 chr7A 75.316 713 148 15 5307 6011 18995841 18996533 4.510000e-82 316.0
54 TraesCS1B01G032200 chr5A 93.056 216 13 2 1 215 688268316 688268530 1.620000e-81 315.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G032200 chr1B 15654288 15662039 7751 False 14316.000000 14316 100.000000 1 7752 1 chr1B.!!$F1 7751
1 TraesCS1B01G032200 chr1B 16176435 16184501 8066 True 781.857143 1869 97.514857 682 7752 7 chr1B.!!$R4 7070
2 TraesCS1B01G032200 chr2B 55033010 55034204 1194 False 1890.000000 1890 95.163000 1761 2959 1 chr2B.!!$F1 1198
3 TraesCS1B01G032200 chr2B 159096124 159097324 1200 True 1760.000000 1760 93.118000 1753 2956 1 chr2B.!!$R1 1203
4 TraesCS1B01G032200 chr2B 246117293 246118350 1057 True 1650.000000 1650 94.816000 1757 2815 1 chr2B.!!$R2 1058
5 TraesCS1B01G032200 chr4B 489980697 489981890 1193 False 1810.000000 1810 93.884000 1756 2965 1 chr4B.!!$F2 1209
6 TraesCS1B01G032200 chr1A 249429907 249431093 1186 True 1735.000000 1735 92.988000 1761 2956 1 chr1A.!!$R4 1195
7 TraesCS1B01G032200 chr1A 12834654 12835770 1116 True 1561.000000 1561 91.829000 4414 5539 1 chr1A.!!$R2 1125
8 TraesCS1B01G032200 chr1A 12855762 12859642 3880 True 610.250000 874 84.210750 213 4419 4 chr1A.!!$R6 4206
9 TraesCS1B01G032200 chr1A 12818164 12818993 829 True 394.250000 708 86.496500 6014 6823 2 chr1A.!!$R5 809
10 TraesCS1B01G032200 chr6B 710067215 710068309 1094 False 1731.000000 1731 95.177000 1757 2854 1 chr6B.!!$F2 1097
11 TraesCS1B01G032200 chrUn 38951748 38952738 990 True 1672.000000 1672 97.082000 1761 2754 1 chrUn.!!$R1 993
12 TraesCS1B01G032200 chr3B 586748093 586749037 944 True 1640.000000 1640 97.989000 1761 2705 1 chr3B.!!$R1 944
13 TraesCS1B01G032200 chr5D 296994267 296995341 1074 True 1639.000000 1639 94.177000 1763 2839 1 chr5D.!!$R1 1076
14 TraesCS1B01G032200 chr7D 18588748 18589440 692 False 322.000000 322 75.490000 5307 6011 1 chr7D.!!$F1 704
15 TraesCS1B01G032200 chr4A 714192239 714192931 692 True 322.000000 322 75.456000 5307 6011 1 chr4A.!!$R2 704
16 TraesCS1B01G032200 chr7A 18995841 18996533 692 False 316.000000 316 75.316000 5307 6011 1 chr7A.!!$F1 704


AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
24 25 0.318699 TTCACGAAGGCACAGACTCG 60.319 55.000 0.00 0.0 0.00 4.18 F
87 88 0.323725 CCACCATGAGTTTGAGGGGG 60.324 60.000 0.00 0.0 38.58 5.40 F
957 1003 0.826062 GCCCATGCATGCTTTTACCT 59.174 50.000 21.69 0.0 37.47 3.08 F
967 1013 5.070001 GCATGCTTTTACCTACATATGGGA 58.930 41.667 11.37 0.0 0.00 4.37 F
2146 2384 1.830408 ATCGGAGCCGGAAGAGAGG 60.830 63.158 5.05 0.0 40.25 3.69 F
2972 3215 0.244178 GAGCTCGGTCGTTCTCCTTT 59.756 55.000 0.00 0.0 0.00 3.11 F
3761 5653 0.036306 AAACAAGGCCGGGTGTAGAG 59.964 55.000 2.18 0.0 0.00 2.43 F
4269 6197 0.030235 CGATACGCGGTCTCATGGAA 59.970 55.000 12.47 0.0 36.03 3.53 F
5161 7089 0.179020 TCAGGAACAAGGCAGGTGTG 60.179 55.000 0.00 0.0 0.00 3.82 F
5487 7415 0.098376 CGTGGTCCACTAGCGTAGTC 59.902 60.000 19.82 0.0 36.76 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1551 1633 1.546029 GGAAATGAGAAGGTTGGGTGC 59.454 52.381 0.00 0.00 0.00 5.01 R
1745 1976 1.578897 TCGGTGAAATCATCCCTGGA 58.421 50.000 0.00 0.00 0.00 3.86 R
2146 2384 2.121538 GGGAGAAATCCCTTGCCGC 61.122 63.158 6.05 0.00 46.39 6.53 R
2965 3208 5.176741 ACGACTAGTCTAGGAAAAGGAGA 57.823 43.478 20.34 0.00 0.00 3.71 R
3179 4270 0.529833 AGTGCATGAGACTCCACTCG 59.470 55.000 0.00 0.00 39.49 4.18 R
4242 6170 0.309922 GACCGCGTATCGAGATCCAA 59.690 55.000 4.92 0.00 41.67 3.53 R
5418 7346 0.031585 CGTAGCTAACAGGCGCCATA 59.968 55.000 31.54 17.28 37.29 2.74 R
5469 7397 0.098376 CGACTACGCTAGTGGACCAC 59.902 60.000 17.43 17.43 39.59 4.16 R
5964 7898 0.317160 TGGCACTCTTGAGTGTACCG 59.683 55.000 25.57 6.65 41.53 4.02 R
7339 9666 0.036671 TCCGTCTGAGTGAGTAGCGA 60.037 55.000 0.00 0.00 0.00 4.93 R


All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)



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AutoCloner maintained by Alex Coulton.